Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Conformational accessibility”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11Linked to original sources
PubMed2003

Proline can have opposite effects on fast and slow protein folding phases.

Proline isomerization is well known to cause additional slow phases during protein refolding. We address a new question: does the presence of prolines significantly affect the very fast kinetics that lead to the formation of folding intermediates? We examined both the very slow (10-100 min) and very fast (4 micro s-2.5 ms) folding kinetics of the two-domain enzyme yeast phosphoglycerate kinase by temperature-jump relaxation. Phosphoglycerate kinase contains a conserved cis-proline in position 204, in addition to several trans-prolines. Native cis-prolines have the largest effect on folding kinetics because the unfolded state favors trans isomerization, so we compared the kinetics of a P204H mutant with the wild-type as a proof of principle. The presence of Pro-204 causes an additional slow phase upon refolding from the cold denatured state, as reported in the literature. Contrary to this, the fast folding events are sped up in the presence of the cis-proline, probably by restriction of the conformational space accessible to the molecule. The wild-type and Pro204His mutant would be excellent models for off-lattice simulations probing the effects of conformational restriction on short timescales.

Enzyme Activation↗
PubMed1989

Recognition in cell adhesion. A comparative study of the conformations of RGD-containing peptides by Monte Carlo and NMR methods.

Many of the proteins that mediate cell adhesion processes processes-fibronectin, fibrinogen, vitronectin, von Willebrand factor, osteopontin, laminin and various collagens--contain the amino acid sequence Arg-Gly-Asp. Short peptides that include this sequence have been shown to inhibit the interactions of cell adhesion proteins with their receptors and to have dramatic effects on developmental processes involving cellular recognition. In order to determine which conformations are accessible to Arg-Gly-Asp containing peptides, we analyzed tri-, tetra- and pentapeptides using molecular mechanics and Monte Carlo methods, and studied the solution conformations of the pentapeptide Gly-Arg-Gly-Asp-Ser using nuclear magnetic resonance techniques. The Monte Carlo method was used to: (a) identify the low energy conformations of the peptides and (b) evaluate their thermodynamic properties. In the case of the pentapeptide Gly-Arg-Gly-Asp-Gly, the four stable conformations include three with reverse turns and one open structure. The conformations found in this analysis are compatible with the nuclear magnetic resonance (nuclear Overhauser effect) data.

Amino Acid Sequence↗
PubMed2004

Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method.

Many proteins change their conformation upon ligand binding. For instance, bacterial periplasmic binding proteins (bPBPs), which transport nutrients into the cytoplasm, generally consist of two globular domains connected by strands, forming a hinge. During ligand binding, hinge motion changes the conformation from the open to the closed form. Both forms can be crystallized without a ligand, suggesting that the energy difference between them is small. We applied Simplicial Neighborhood Analysis of Protein Packing (SNAPP) as a method to evaluate the relative stability of open and closed forms in bPBPs. Using united residue representation of amino acids, SNAPP performs Delaunay tessellation of the protein, producing an aggregate of space-filling, irregular tetrahedra with nearest neighbor residues at the vertices. The SNAPP statistical scoring function is derived from log-likelihood scores for all possible quadruplet compositions of amino acids found in a representative subset of the Protein Data Bank, and the sum of the scores for a given protein provides the total SNAPP score. Results of scoring for bPBPs suggest that in most cases, the unliganded form is more stable than the liganded form, and this conclusion is corroborated by similar observations of other proteins undergoing conformation changes upon binding their ligands. The results of these studies suggest that the SNAPP method can be used to predict the relative stability of accessible protein conformations. Furthermore, the SNAPP method allows delineation of the role of individual residues in protein stabilization, thereby providing new testable hypotheses for rational site-directed mutagenesis in the context of protein engineering.

Amino Acids↗
PubMed1980

Thermal perturbation differential spectra of ribonucleic acids. III. Chain length effect.

Thermal perturbation differential spectra of several adenylic acid oligomers, two single-strand polyribonucleotides, poly(A) and poly(C), and five trinucleoside diphosphates, U-A-A, U-A-G, U-G-A, C-U-C and C-U-A, were obtained and analysed. It is shown that these differential spectra cannot be entirely described by the nearest-neighbour approximation devised from the appropriate mononucleotides and dinucleoside monophosphates. In an attempt to determine the origin of this discrepancy, we have examined the possible optical changes arising from increased electronic interactions, changes in conformation, solvent accessibility or thermodynamic properties. This study indicates that dinucleoside monophosphates on one the hand and trinucleoside diphosphates on the other hand, are separate classes from the conformational point of view. The capacity to assume stacks, absent or negligible in higher oligomers or polymers, makes them poor models for the stacking interaction in longer nucleic acids. It is also shown that in trinucleoside diphosphates, interaction between the two terminal bases arising from bulging out of the middle base is very likely to occur. This type of interaction has to be taken into account in the description of the temperature perturbation differential spectra of trimers.

Macromolecular Substances↗
PubMed2004

Entropy effects on protein hinges: the reaction catalyzed by triosephosphate isomerase.

Many proteins utilize segmental motions to catalyze a specific reaction. The Omega loop of triosephosphate isomerase (TIM) is important for preventing the loss of the reactive enediol(ate) intermediate. The loop opens and closes even in the absence of the ligand, and the loop itself does not change conformation during movement. The conformational changes are localized to two hinges at the loop termini. Glycine is never observed in native TIM hinge sequences. In this paper, the hypothesis that limited access to conformational space is a requirement for protein hinges involved in catalysis was tested. The N-terminal hinge was mutated to P166/V167G/W168G (PGG), and the C-terminal hinge was mutated to K174G/T175G/A176G (GGG) in chicken TIM. The single-hinge mutants PGG and GGG had k(cat) values 200-fold lower than that of the wild type and K(m) values 10-fold higher. The k(cat) of double-hinge mutant P166/V167G/W168G/K174G/T175G/A176G was reduced 2500-fold; the K(m) was 10-fold higher. A combination of primary kinetic isotope effect measurements, isothermal calorimetric measurements, and (31)P NMR spectroscopic titration with the inhibitor 2-phosphoglycolate revealed that the mutants have a different ligand-binding mode than that of the wild-type enzyme. The predominant conformations of the mutants even in the presence of the inhibitor are loop-open conformations. In conclusion, mutation of the hinge residues to glycine resulted in the sampling of many more hinge conformations with the consequence that the population of the active-closed conformation is reduced. This reduced population results in a reduced catalytic activity.

Animals↗
PubMed2002

Origin of enantiomeric selectivity in the aryloxyphenoxypropionic acid class of herbicidal acetyl coenzyme A carboxylase (ACCase) inhibitors.

Molecular modeling was used to propose an "active conformation" for the R-2-phenoxypropionic acid portion of the aryloxyphenoxypropionic acid series of herbicidal acetyl CoA carboxylase (ACCase) inhibitors. This candidate active conformation is a low-energy conformer with the R-methyl distal to the phenoxy fragment, stabilized by the generalized anomeric effect around the propionate ether bond; the inactive S-enantiomer has difficulty accessing this conformation due to steric interaction of the S-methyl with the o-hydrogen of the phenyl. This candidate conformation was challenged by preparation of a series of novel rigid analogues. ACCase inhibition data suggest that the systems which contain a fused five-membered, but not a six-membered, ring present the necessary pharmacophore to the active site of ACCase, confirming the active conformation hypothesis and demonstrating that the precise placement of the carboxylate relative to the phenyl group is more critical than the placement of the methyl.

Acetyl-CoA Carboxylase↗
PubMed1997

NMR structural characterization of oligo-N-substituted glycine lead compounds from a combinatorial library.

Synthesis and screening of combinatorial libraries for pharmaceutical lead discovery is a rapidly expanding field. Oligo-N-substituted glycines (NSGs) were one of the earliest sources of molecular diversity in combinatorial libraries. In one of the first demonstrations of the power of combinatorial chemistry, two NSG trimers, CHIR-2279 and CHIR-4531, were identified as nM ligands for two 7-transmembrane G-protein-coupled receptors. The NMR characterization of these two lead compounds was undertaken to verify covalent connectivity and to determine solution conformations, if any. The sequential chemical shift assignments were performed using a new strategy for assigning 1H and 13C resonances of NSGs. The conformational preferences were then determined in both an aqueous co-solvent system and an organic solvent to probe the effects of hydrophobic collapse. NSGs are expected to be more flexible than peptides due to the tertiary amide, with both cis and trans amide bond conformations being accessible. Solution NMR studies indicate that although CHIR-2279 and CHIR-4531 have identical backbones and termini, and very similar side chains, they do not display the same solution conformational characteristics.

Dimethyl Sulfoxide↗
PubMed2005

Conformational rigidification via derivatization facilitates the determination of absolute configuration using chiroptical spectroscopy: a case study of the chiral alcohol endo-borneol.

We demonstrate that derivatization of the OH group of endo-borneol, 1, leads to conformational rigidification. Conformational analysis (CA) of 1 and its methyl, acetate, tert-butyl, and trimethylsilyl derivatives, 2-5, is carried out using ab initio density functional theory (DFT). The number of thermally accessible stable conformations is reduced from 3 in 1, to 2 in 2, and to 1 in 3-5. Comparison of IR and vibrational circular dichroism (VCD) spectra of 1 and 3-5, calculated using DFT, to experimental spectra unambiguously confirms the DFT CA. The determination of absolute configurations (ACs) of chiral molecules via analysis of chiroptical spectra using DFT methods increases in complexity and decreases in reliability as the number of populated conformations increases. Our results for endo-borneol support the conclusion that, in the case of chiral alcohols, derivatization can lead to substantial rigidification and, as a result, significantly facilitate the determination of ACs.

Camphanes↗
PubMed2006

The backrub motion: how protein backbone shrugs when a sidechain dances.

Surprisingly, the frozen structures from ultra-high-resolution protein crystallography reveal a prevalent, but subtle, mode of local backbone motion coupled to much larger, two-state changes of sidechain conformation. This "backrub" motion provides an influential and common type of local plasticity in protein backbone. Concerted reorientation of two adjacent peptides swings the central sidechain perpendicular to the chain direction, changing accessible sidechain conformations while leaving flanking structure undisturbed. Alternate conformations in sub-1 angstroms crystal structures show backrub motions for two-thirds of the significant Cbeta shifts and 3% of the total residues in these proteins (126/3882), accompanied by two-state changes in sidechain rotamer. The Backrub modeling tool is effective in crystallographic rebuilding. For homology modeling or protein redesign, backrubs can provide realistic, small perturbations to rigid backbones. For large sidechain changes in protein dynamics or for single mutations, backrubs allow backbone accommodation while maintaining H bonds and ideal geometry.

Algorithms↗
PubMed1997

Does an open access system properly utilize endoscopic resources?

BACKGROUND: In an effort to maintain procedure volumes and control consultation costs, many gastrointestinal endoscopists and primary care providers have implemented systems of open access endoscopy. In these systems, specialists in digestive diseases perform endoscopy without prior consultation. The purpose of this study is to determine if indications for upper endoscopic procedures requested in an open access system conform to national practice guidelines and to establish the yield of diagnostic information relevant for patient care in this system. METHODS: Procedural indications and results for 3715 upper endoscopic procedures performed in an open access system were recorded in a computer database. The practice guideline "Appropriate Use of Gastrointestinal Endoscopy" (AUGE) of the American Society for Gastrointestinal Endoscopy was used to determine appropriateness of procedural indications. RESULTS: Eighty-four percent of procedures were performed for indications listed in the AUGE, and 59% resulted in findings relevant to patient care. Specialists requested endoscopy more frequently for "approved" indications than did nonspecialists (p = .004) and more frequently had findings relevant to patient care (p < .001). Findings relevant to patient care are significantly more frequent for some indications listed in the AUGE compared to others (p < .001). CONCLUSIONS: Adherence to practice guidelines can and does occur in an open access system. Specialists request endoscopy more frequently for appropriate indications compared to nonspecialists and have a higher yield of information relevant to patient care. Further refinement and better definition of some indications within the AUGE are needed to increase the clinical utility of this document.

Endoscopy, Gastrointestinal↗
PubMed2004

beta-hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution.

The structural properties of a 10-residue and a 15-residue peptide in aqueous solution were investigated by molecular dynamics simulation. The two designed peptides, SYINSDGTWT and SESYINSDGTWTVTE, had been studied previously by NMR at 278 K and the resulting model structures were classified as 3:5 beta-hairpins with a type I + G1 beta-bulge turn. In simulations at 278 K, starting from the NMR model structure, the 3:5 beta-hairpin conformers proved to be stable over the time period evaluated (30 ns). Starting from an extended conformation, simulations of the decapeptide at 278 K, 323 K and 353 K were also performed to study folding. Over the relatively short time scales explored (30 ns at 278 K and 323 K, 56 ns at 353 K), folding to the 3:5 beta-hairpin could only be observed at 353 K. At this temperature, the collapse to beta-hairpin-like conformations is very fast. The conformational space accessible to the peptide is entirely dominated by loop structures with different degrees of beta-hairpin character. The transitions between different types of ordered loops and beta-hairpins occur through two unstructured loop conformations stabilized by a single side-chain interaction between Tyr2 and Trp9, which facilitates the changes of the hydrogen-bond register. In agreement with previous experimental results, beta-hairpin formation is initially driven by the bending propensity of the turn segment. Nevertheless, the fine organization of the turn region appears to be a late event in the folding process.

Amino Acid Sequence↗
PubMed2005

Functional plasticity in the substrate binding site of beta-secretase.

The aspartic protease beta-secretase (BACE) cleaves the amyloid precursor protein into a 42 residue beta-peptide, which is the principal biochemical marker of Alzheimer's disease. Multiple explicit-water molecular dynamics simulations of the apo and inhibitor bound structures of BACE indicate that both open- and closed-flap conformations are accessible at room temperature and should be taken into account for inhibitor design. Correlated motion is observed within each of the two lobes of BACE, as well as for the interfacial region. A self-inhibited conformation with the side chain of Tyr71 occupying the S(1) pocket is present in some of the unbound simulations. The reversible loss of the side chain hydrogen bond between the catalytic Asp32 and Ser35, due to the concomitant reorientation of the Ser35 hydroxyl group and a water molecule conserved in pepsin-like enzymes, provides further evidence for the suggestion that Ser35 assists in proton acceptance and release by Asp32 during catalysis.

Alzheimer Disease↗
PubMed1995

A helical epitope in the C4 domain of HIV glycoprotein 120.

The fourth conserved domain of the human immunodeficiency virus type 1 (HIV-1) envelope, the C4 region of glycoprotein 120 (gp120), is an amphipathic stretch of amino acids that, based on mutational analyses, constitutes a major component of the CD4 binding region in gp120. In the absence of crystallographic and NMR data on C4 in intact gp120, we sought to gain insight into C4's conformation and accessibility in gp120 by taking an immunochemical approach. In this study, a peptomer composed of a repeat peptide of C4 amino acids 419-436 from gp120 of HIV-1MN was synthesized for use as a conformationally constrained immunogen. Circular dichroism studies disclosed that the polymerized peptide, peptomer-(419-436), in 0.01 M Na2HPO4 buffer, pH 7.4, at 25 degrees C contained a dominant alpha-helical structure (53 +/- 1%) compared with 2 +/- 4% alpha-helical content for the monomeric peptide-(419-436). The peptomer in Ribi's adjuvant induced the production of rabbit antibodies that recognized recombinant and native gp120 but, consistent with the literature, the C4 peptide having no conformational constraints did not. The experimental results show that only those antibodies formed against a helical immunogen from C4 will recognize recombinant and native gp120, and, therefore, the results support the notion that C4 is an alpha-helix in gp120.

Amino Acid Sequence↗
PubMed2026

Refining sequence-to-expression modelling with chromatin accessibility.

MOTIVATION: Sequence-to-expression models typically do not consider chromatin accessibility, a major factor limiting gene regulation. We hypothesized that supplying accessibility as an input feature would allow a sequence-to-expression model to focus on important open regions of the genome. RESULTS: We found that the performance of such an augmented model was significantly better than that of sequence-only or accessibility-only models with similar architectures. Specifically, its ability to predict the expression of highly variable genes and gene expression in other cell types improved, and higher attribution scores in the input DNA sequences of the augmented model conformed to accessibility, enabling the learning of cell type-specific sequence patterns. Additionally, we show that fine-tuning a pre-trained sequence-only model with both sequence and accessibility can boost performance further and highlight the importance of sequencing depth in sequence-to-expression prediction. AVAILABILITY AND IMPLEMENTATION: Source code is available on GitHub at https://github.com/lapohosorsolya/accessible_seq2exp.

Chromatin↗
PubMed1992

Conformational stability of a thrombin-binding peptide derived from the hirudin C-terminus.

The COOH-terminal region of hirudin represents an independent functional domain that binds to an anion-binding exosite of thrombin and inhibits the interaction of thrombin with fibrinogen and regulatory proteins in blood coagulation. The thrombin-bound structure of the peptide fragment, hirudin 55-65, has been determined by use of transferred NOE spectroscopy [Ni, F., Konishi, Y., & Scheraga, H. A. (1990) Biochemistry 29, 4479-4489]. The stability of the thrombin-bound conformation has been characterized further by a combined NMR and theoretical analysis of the conformational ensemble accessible by the hirudin peptide. Medium- and long-range NOE's were found for the free hirudin peptide in aqueous solution and in a mixture of dimethyl sulfoxide and water at both ambient (25 degrees C) and low (0 degrees C) temperatures, suggesting that ordered conformations are highly populated in solution. The global folding of these conformations is similar to that in the thrombin-bound state, as indicated by NOE's involving the side-chain protons of residues Phe(56), Ile(59), Pro(60), Tyr(63), and Leu(64). Residues Glu(61), Glu(62), Tyr(63), and Leu(64) all contain approximately 50% of helical conformations calculated from the ratio of the sequential dNN and d alpha N NOE's. Among the helical ensemble, active 3(10)-helical conformations were found by an analysis of the medium-range [(i,i+2) and (i,i+3)] NOE's involving the last six residues of the peptide. An analysis of the side-chain rotamers revealed that, upon binding to thrombin, there may be a rotation around the alpha CH-beta CH bond of Ile(59) such that Ile(59) adopts a gauche- (chi 1 = +60) conformation in contrast to the highly populated trans (chi 1 = -60) found for Ile(59) in the free peptide. However, the thrombin-bound conformation of the hirudin peptide is still an intrinsically stable conformer, and the preferred conformational ensemble of the peptide contains a large population of the active conformation. The apparent preference for a gauche- (chi 1 = +60) side-chain conformation of Ile(59) in the bound state may be explained by the existence of a positively charged arginine residue among the hydrophobic residues in the thrombin exosite.

Binding Sites↗
PubMed1994

Ligand docking to proteins with discrete side-chain flexibility.

An algorithm is described that explores the conformational degrees of freedom of the amino acid side-chains and of the ligand when docking a putative ligand into a receptor site. For a given orientation of the ligand relative to the protein, the method can find the lowest energy combination of amino acid side-chains and ligand conformations as well as all other combinations in order of increasing energy within a specified energy cutoff. The amino acid side-chains and the ligand are restricted to discrete low-energy conformations, determined for the former by analysing high-resolution protein structures and in the latter case from a conformational analysis. Coupled to an algorithm for exploring the six degrees of orientational freedom of the ligand with respect to the receptor, the method can be used to perform conformationally flexible ligand docking. A combination of two search methods is employed to explore the conformational degrees of freedom: Dead End Elimination and the A* algorithm. When no ligand is present the approach can be used to predict the lowest energy combinations of side-chain conformations for a given protein backbone structure. The approach is employed to illustrate how such a procedure can be used to estimate the conformational entropy change that accompanies the formation of an intermolecular complex between a protein and a ligand and to demonstrate that the protein's conformational entropy may in some cases increase on binding the ligand. This is due to a modification of the protein's energy hypersurface that makes more conformational states accessible. Our results highlight the need for appropriate methods to estimate the strength of binding.

Algorithms↗
PubMed1995

Relativity of an antigenic homology between human interferon-alpha 1 and interferon-alpha 2c.

Analysis of an antigenic relatedness between human interferon (IFN)-alpha 1 and IFN-alpha 2 was performed with mapped monoclonal antibodies raised to the respective subtypes. Antigenic properties of immunoreactive domains located in the N-terminal segments 30-67 of IFN-alpha 1 and IFN-alpha 2 were found distinct when compared by neutralization bioassay or ELISA. On the other hand, corresponding domains exhibited an unexpectedly high antigenic homology when tested by Western blot. We suppose that this relativity in antigenic relation lies in the various extent of denaturation of IFN-molecules in bioassay, ELISA and immunoblot. Structural differences of tested antigens may be responsible for a conformation-determined access of antibodies to the shared epitopes.

Amino Acid Sequence↗
PubMed1994

Calcium ion binding regions in C-reactive protein: location and regulation of conformational changes.

C-reactive protein (CRP) is a pentameric acute phase serum protein composed of identical 206 amino acid subunits that associate by non-covalent bonds. The biological activities ascribed to CRP are initiated by binding ligands via the single PC-binding site within each subunit. CRP binding to PC requires a conformational change in the intact pentraxin triggered by the binding of two free Ca2+ ions per subunit. Residues 134-148 of each subunit were previously implicated by indirect measures as one of the Ca(2+)-binding sites. In this study, 45Ca2+ autoradiography revealed that fragments of CRP of 6.5 and 16 kDa generated by proteolysis between residues 146 and 147 bind Ca2+ indicating that a second Ca(2+)-binding site is located within the C-terminal 60 amino acids. Synthetic peptides corresponding to residues 134-148 and 152-176 both bound 45Ca2+ in equilibrium dialysis experiments with a Kd = 5.2 x 10(-4) and 1.7 x 10(-4) M, respectively. The addition of Ca2+ to peptide 152-176 induced a shift in the CD-spectra between 210 and 230 nm. Rabbit anti-peptide 152-176 antibody (Ab) inhibited the availability of an epitope within the PC-binding site of CRP recognized by mAb EA4-1. Reactivity of CRP with both anti-peptide 134-148 mAb and anti-peptide 152-176 Ab enhanced the expression of the PC-binding site epitope. The results suggest that the two distinct Ca(2+)-binding sites within each CRP subunit are composed of residues 134-148 and 152-176 and that these two nearly adjacent sites cooperate to exert an allosteric change in conformation allowing access to the PC-binding site.

Allosteric Regulation↗